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Genome of the candidate phylum Aminicenantes bacterium from a deep subsurface thermal aquifer revealed its fermentative saccharolytic lifestyle

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Abstract

Bacteria of candidate phylum OP8 (Aminicenantes) have been identified in various terrestrial and marine ecosystems as a result of molecular analysis of microbial communities. So far, none of the representatives of Aminicenantes have been isolated in a pure culture. We assembled the near-complete genome of a member of Aminicenantes from the metagenome of the 2-km-deep subsurface thermal aquifer in Western Siberia and used genomic data to analyze the metabolic pathways of this bacterium and its ecological role. This bacterium, designated BY38, was predicted to be rod shaped, it lacks flagellar machinery but twitching motility is encoded. Analysis of the BY38 genome revealed a variety of glycosyl hydrolases that can enable utilization of carbohydrates, including chitin, cellulose, starch, mannose, galactose, fructose, fucose, rhamnose, maltose and arabinose. The reconstructed central metabolic pathways suggested that Aminicenantes bacterium BY38 is an anaerobic organotroph capable of fermenting carbohydrates and proteinaceous substrates and performing anaerobic respiration with nitrite. In the deep subsurface aquifer Aminicenantes probably act as destructors of buried organic matter and produce hydrogen and acetate. Based on phylogenetic and genomic analyses, the novel bacterium is proposed to be classified as Candidatus Saccharicenans subterraneum.

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Acknowledgements

This work was performed using the scientific equipment of the Core Research Facility ‘Bioengineering’ (Research Center of Biotechnology RAS) and supported by the Russian Science Foundation (Grant no. 14-14-01016).

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Authors and Affiliations

  1. Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Prosp 33-2, Moscow, 119071, Russia

    Vitaly V. Kadnikov, Andrey V. Mardanov, Alexey V. Beletsky & Nikolai V. Ravin

  2. Laboratory of Biochemistry and Molecular Biology, Tomsk State University, 634050, Tomsk, Russia

    Olga V. Karnachuk

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  1. Vitaly V. Kadnikov
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  2. Andrey V. Mardanov
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  3. Alexey V. Beletsky
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  4. Olga V. Karnachuk
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  5. Nikolai V. Ravin
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Correspondence to Nikolai V. Ravin.

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Communicated by S. Albers.

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Kadnikov, V.V., Mardanov, A.V., Beletsky, A.V. et al. Genome of the candidate phylum Aminicenantes bacterium from a deep subsurface thermal aquifer revealed its fermentative saccharolytic lifestyle. Extremophiles 23, 189–200 (2019). https://doi.org/10.1007/s00792-018-01073-5

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